• Does the proportion of human cases attributed to each source change seasonally?

• Did the intervention in the poultry industry work?

• Is attribution related to rurality?

• Do some genotypes cause human disease more than others?

Work with Poppy Miller and Chris Jewell, generalising the modified Hald model of Müllner et. al. 2009.

Model human cases \(Y_{itl}\) of genotype \(i\) at time \(t\) in location \(l\) by \[ Y_{itl} \sim \mathsf{Poisson}(q_i \sum_j a_{jtl} p_{ijt}) \]

• \(a_{jtl}\) captures propensity of source \(j\) to act as a vehicle for disease at time \(t\) in location \(l\).
• \(p_{ijt}\) is the relative occurrence of type \(i\) on source \(j\) at time \(t\).
• \(q_i\) captures propensity of genotype \(i\) to be over-represented in human cases.

Nested within each source \(j\) we have \[ \begin{aligned} \mathsf{logit}\left(P(\mathsf{source}_j \mid t, \mathbf{x})\right) &= \mathsf{Location}_\mathbf{x} \cdot \mathbf{1}\left[t \geq 2008\right] \cdot \mathsf{Month}_t + \epsilon_{\mathbf{x}t}\\ \epsilon_{\mathbf{x}t} &\sim \mathsf{Normal}(\rho \epsilon_{\mathbf{x}(t-1)}, \sigma^2) \end{aligned} \]

• Covariates are estimated as a Gibbs step conditional on correlation \(\rho\), variance \(\sigma^2\) and \(P(\mathsf{source}_j \mid t, \mathbf{x})\).

• \(\phi\) and \(\sigma^2\) are then updated using Gibbs conditional on the covariates and \(P(\mathsf{source}_j \mid t, \mathbf{x})\).

• \(P(\mathsf{source}_j \mid t, \mathbf{x})\) are then updated from the full conditional prior, interleaved with Metropolis Hastings steps.

• Urban cases tend to be more associated with poultry, and rural cases with ruminants.

• There does seem to be some evidence for seasonality in attribution.

• The poultry intervention in 2007 resulted in a marked reduction in poultry related cases in urban areas, less strong in rural areas.

• Very few cases associated with water or other sources.

• Limitation: Genomic model assumed constant through time.

• Two R packages are on the way, sourceR and islandR.

• MidCentral Public Health Services: Tui Shadbolt,
  Adie Transom
• Medlab Central: Lynn Rogers
• ESR: Phil Carter
• mEpiLab: Rukhshana Akhter, Julie Collins-Emerson,
  Ahmed Fayaz, Anne Midwinter, Sarah Moore, Antoine Nohra, Angie Reynolds
• Ministry for Primary Industries: Donald Campbell,
  Peter van der Logt
• Poppy Miller, Chris Jewell
• Petra Müllner
• Nigel French